As some of you know, The Bioperl project (http://bio.perl.org) is a
coordinated effort to collect computational methods routinely used in
bioinformatics into a set of standard, well-documented, and freely
available Perl modules. The latest version, bioperl-0.04.1 has recently
been made available. Some of us are now focussing on the design of a 3D
structure object for use in Perl-based bioinformatics applications.
Although small molecules shall be supported if/when they interact with
biological macromolecules, the main focus is on macromolecular structures.
We would like to open the general issue to discussion, your ideas and
suggestions at this stage. Among others, we would especially like to hear
your comments on the following areas:
- In what sort of program would you use such a module?
- How would you want to access the data, and what methods should be
available?
Responses from this message will be employed to create a requirements
specification for the design of a 3D macromolecular structure object. Such
requirements will aid the design of 3D structure modules within the
Bioperl project.
The preliminary page has been set up and an Initial Requirements List was
prepared primarily by one of us (Steve Chervitz) at:
http://bio.perl.org/Projects/Structure/requirements.html
to further compile such requirements and consolidate structure-related
issues at the moment. Any other ideas/suggestions/contributions will be
appreciated. Please direct responses to the bioperl discussion mailing
list: vsns-bcd-perl at lists.uni-bielefeld.de. Thank you.
Eser Ayanoglu
Doug Brutlag Bioinformatics Group
Dept. of Biochemistry
Stanford University
Steve Chervitz
Bioperl Coordinator
Neomorphic Software, Berkeley, CA
Steven Brenner
Dept. of Structural Biology
Stanford University